For the installation,
1) Download eclipse 4.3.1(Kepler) from //www.eclipse.org/downloads, extract it, start eclipse.
2) Install PDT thru 'Install New Software' from preconfigured Kepler repository.(//download.eclipse.org/releases/kepler)
That's all. What kind of difficulty is there.
Even if you choosed the eclipse package in Ubuntu repository,(note that it is 3.7.2(Indigo) based)
1) Install eclipse with Software Manager or Package Manager, start eclipse.
2) Install PDT thru 'Install New Software' from preconfigured Indigo repository.(//download.eclipse.org/releases/indigo)
That's all. What kind of difficulty is there. Even though you'll get PDT 3.0.1 in this case.

>Software being installed: PHP Development Tools (PDT) 3.1.2.201212211235 (org.eclipse.php.feature.group 3.1.2.201212211235)
You are going to install PDT 3.1.2, and it is for/in Eclipse 3.8/4.2(Juno). You need to add Juno repository in 'Available Software Sites'.
If you had installed eclipse from Ubuntu repository and you had added the abandoned update site //download.eclipse.org/tools/pdt/updates/release (in accordance with the abandoned page //www.eclipse.org/pdt/downloads/), you'll encounter this dependency problem. Because it is wrong.